Whoof, this is gonna be a tough one.

Final Fantasy: Final Fantasy X
Suikoden: Suikoden II
Breath of Fire: Breath of Fire III
Legend of Legaia: Legend of Legaia
Baldur's Gate: Baldur's Gate II: Shadows of Amn
Sonic the Hedgehog: Sonic the Hedgehog 2
Age of Empires: Age of Empires II: Age of Kings
Assassin's Creed: Assassin's Creed IV
Dead Rising: Dead Rising
Deus Ex: Deus Ex
The Elder Scrolls: TES III: Morrowind
Total War: Rome: Total War (Though I think Shogun 2 is actually the best, I enjoy Rome I the most)
Grand Theft Auto: GTA: San Andreas
Saint's Row: Saint's Row 2
SimCity: SimCity 4
Space Empires: Space Empires V
X-Com: X-Com: UFO Defense
Fallout: Fallout (but New Vegas comes damn close)
Little Big Adventure: Little Big Adventure 2: Twinsen's Adventure
Populous: Populous: The Beginning
Rollercoaster Tycoon: Rollercoaster Tycoon 2 (but 1 has the best scenarios by far)
Theme: Theme Hospital
Diablo: Diablo 2
Warcraft: Warcraft 3
Command & Conquer: Red Alert 2
Mario: Super Mario 64
Pokemon: Pokemon X/Y
Civilization: Civilization IV
Star Ocean: Star Ocean 2